Nevertheless, here is some information, how a feature could become orphaned:
Most often, a feature was installed (e.g. via a solution, STSADM or Visual Studio), then the solution was removed without cleanly removing the feature.

(E.g. when you remove a solution containing a web scoped feature, the feature stays activated in the web. If you then deploy an updated version of the solution, the feature is active, without being activated again. This is useful e.g. for list instance features.
It would delete the whole list, if the feature would automatically be deactivated when removing the solution)